Chapter 35:
Molecular Detection and Characterization of HIV-1

Affiliations: 1: Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322;
2: Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322

This chapter focuses on the available molecular tests for diagnosis, monitoring, and management of HIV-1-infected individuals. It also focuses on molecular methods as they apply to the diagnosis and management of human immunodeficiency virus type 1 (HIV- 1). The guidelines for initiation of therapy based on viral load have changed as one's understanding of disease progression at higher CD4 cell counts has improved. Combination therapy using drugs from multiple classes has been the most effective approach to controlling viral replication. There are several FDA-approved assays for the detection, quantification, and characterization of HIV-1, and this field has expanded recently with the approval of real-time RTPCR viral load tests. A section covers conventional and real-time viral load tests, RNA and proviral DNA tests for the detection of HIV-1, resistance testing, and the tropism assay. The Amplicor monitor test was modified in a study comparing viral load values between the conventional and real-time tests using a different extraction method than recommended by the manufacturer, and it is unclear what impact this may have had on the viral load values. The current recommendations for specimen collection and processing for HIV-1 resistance testing are the same as for viral load testing. Genotypic resistance testing is one of the most complex tests performed in the molecular microbiology laboratory and involves multiple technical steps to generate the sequence as well as interpretation of the sequencing data. Currently, the systems for viral load testing require high capital investment in instrumentation along with reliable electricity and pure water.